Predicting sequences and structures of MHC-binding peptides: a computational combinatorial approach.

Peptides bound to MHC molecules on the surface of cells convey critical information about the cellular milieu to immune system T cells. Predicting which peptides can bind an MHC molecule, and understanding their modes of binding, are important in order to design better diagnostic and therapeutic agents for infectious and autoimmune diseases. Due to the difficulty of obtaining sufficient experimental binding data for each human MHC molecule, computational modeling of MHC peptide-binding properties is necessary. This paper describes a computational combinatorial design approach to the prediction of peptides that bind an MHC molecule of known X-ray crystallographic or NMR-determined structure. The procedure uses chemical fragments as models for amino acid residues and produces a set of sequences for peptides predicted to bind in the MHC peptide-binding groove. The probabilities for specific amino acids occurring at each position of the peptide are calculated based on these sequences, and these probabilities show a good agreement with amino acid distributions derived from a MHC-binding peptide database. The method also enables prediction of the three-dimensional structure of MHC-peptide complexes. Docking, linking, and optimization procedures were performed with the XPLOR program [1].

The L6 membrane proteins--a new four-transmembrane superfamily.

L6, IL-TMP, and TM4SF5 are cell surface proteins predicted to have four transmembrane domains. Previous sequence analysis led to their assignment as members of the tetraspanin superfamily. In this paper, we identify a new sequence (L6D) that is strikingly similar to L6, IL-TMP, and TM4SF5. Analyses of these four sequences indicate that they are not significantly related to genuine tetraspanins, but instead constitute their own L6 superfamily.

The nonpolymorphic MHC class II isotype, HLA-DQA2, is expressed on the surface of B lymphoblastoid cells.

The more centromeric of the two human MHC class II DQA genes, DQA2, has not previously been shown to express a protein product. However, its high degree of sequence similarity to DQA1, the fact that it is highly evolutionarily conserved, and the recent demonstration of its transcription in some cell lines suggest that a DQA2 alpha-chain may be expressed. Polyclonal anti-peptide antisera were generated and shown to be specific for DQA2 in Western blotting of Triton X-114 preparations of B lymphoblastoid cell lines. DQA2 expression is variable, although always at least threefold less than that of DQA1, and is found in all haplotypes examined. Immunoprecipitations of biotin-labeled cell surface proteins reveal that DQA2 appears at the cell surface. In keeping with others' findings, no evidence for an expressed DQB2 beta-chain was found, prompting investigation of the means by which DQA2 gains access to the cell surface. Antisera specific for allotypic and isotypic MHC class II beta-chains were used in sequential immunoprecipitation experiments to search for a beta-chain partner for DQA2, and a transfectant system was established in an attempt to promote pairing of DQA2 with a selected DQB1 (*0501) chain. In neither case was DQA2 found to dimerize with an MHC class II beta-chain. Despite this, DQA2 is capable of forming a complex with invariant chain.

Temporal discontinuities in progression of NOD autoimmune diabetes.

Consideration of the pathophysiology of insulin-dependent diabetes mellitus in the nonobese diabetic (NOD) mouse can be viewed from a temporal perspective. We argue that there are discontinuous phases and each phase may reflect a phenotype educed by a particular set of genetic and epigenetic events. Therefore, temporal dissection may be a useful platform for causal dissection and we have set out this article as follows: 1. Introduction. 2. "Pre-time." a. Genetics. b. Parental effects. 3. Development of insulitis. a. Development of autoimmunity vs waning of or failure to establish tolerance. b. Importance of beta cell mass. c. Homing. 4. Onset of beta cell destruction. 5. Further Discussion.